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Author SHA1 Message Date
Jostein Bø Fløystad 7afae271dd Add contributors for phase unwrapping. 2013-11-22 12:59:35 +01:00
Jostein Bø Fløystad 51f94d83a9 Less verbose entry in CONTRIBUTORS. 2013-11-22 12:29:31 +01:00
Jostein Bø Fløystad ccbd3bfced unwrap: Do not include debug symbols in extension builds. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 37b5a946c8 unwrap tests: PEP8 fixes. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 38d502208f unwrap example: Include masking and wrap around. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 3737e6ebd3 unwrap example: Mention dimensionalities available. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad a10f1c1468 unwrap example: cleanup. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 8ad3d1df17 unwrap: Simplify code after completing float->double. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 593a7d63ce unwrap: Change 1D unwrapper from float to double. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad cd5cc84aa9 unwrap: Change 3D wrapper code from float to double. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad d0ccbe71c1 unwrap: Change 3D C code from float to double. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 9091d2759a unwrap: Change 2D wrapper code from float to double. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 9bacb0d54a unwrap: Use UNIX line endings. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad ebf457cea8 unwrap: Convert 2D C code from float to double. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad a6e7bd4a00 unwrap: Use constants from math.h in C code. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad f53a4e0764 unwrap: Add naive 1D unwrapper. 
The naive 1D unwrapper does not support masked arrays because the
1D unwrapping problem has an infite number of solutions when faced with
missing data. Wrap around is not implemented because 1D phase unwrapping
must start at a certain pixel, and there will always be a risk of a
discontinuity there, wrap around or not.
 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad f87fadf0f0 unwrap: Rename C files. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad b2ac1a5872 unwrap: Add docstring example. 2013-11-22 10:45:07 +01:00
Jostein Bø Fløystad 27c13a1193 unwrap: Warn about singleton dimensions in 3D arrays. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 781ead2c9f unwrap: Rename function unwrap() -> unwrap_phase(). 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 4cfec880b6 unwrap: Small style-like fixes. 
Based on comments by ahojnnes.
 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad e0b7fe32a1 unwrap: PEP8 fixes. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 3ddd94a89c unwrap: Simplify example. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 9e50686c8f unwrap: Add test for unwrapping masked images. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 8a93677db0 unwrap: Delete "example" from the test file. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad c0d0984049 unwrap: Make sure test data wraps along all dimensions. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 619da811d8 unwrap: Reduce code duplication. 
Use the yield functionality in nose to minimize setup.
 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad b0c21ea972 unwrap: Reduce duplication in tests. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 43d110627b unwrap: PEP8 fixes. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad b9f119a428 unwrap: Python 3 compatibility. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad a39695154f unwrap: Update bento.info. 2013-11-22 10:45:06 +01:00
Jostein Bø Fløystad 9644ed5655 unwrap: rename variables in cython extensions 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad 5022cfb699 unwrap: PEP8 fixes for cython extensions. 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad 676ba5a07e unwrap: rename cython functions. 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad e8fa4998ad unwrap: Whitespace fixes and comment removal. 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad 12268ff555 unwrap: Refactor and fix wrap around functionality. 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad 6dbe6965e6 unwrap: Test wrap_around functionality. 
This test is currently failing. Most likely, the axes are swapped.
 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad 0e8be31ba6 unwrap: Simplify handling of masked arrays. 2013-11-22 10:42:29 +01:00
Jostein Bø Fløystad ac330662b9 unwrap: Remove unused imports 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 54865ecb23 unwrap: reformat references 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad ebef821a70 unwrap: Add citation for 3D. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 0e56ee9577 unwrap: Remove plotting code. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 8a81624ba8 unwrap: Format references correctly. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 2f784366b7 unwrap: Correct use of relative imports. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad a2a6f8d4b5 unwrap: Use relative imports 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 5bfbd7cdad Add example for phase unwrapping. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 37f36cd98b unwrap: Add docstring. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 26138fbeb6 unwrap: Refactor to skimage-style variable names. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad b29dd83eea unwrap: Refactor wrap_around argument. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 933e2c77f3 unwrap: Add unfinished docstrings. 
Conflicts:
	skimage/exposure/unwrap.py
 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad f67b03643a unwrap: Fix whitespace in c code. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad e72e5de06e unwrap: Move imports to module level. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad d2fb06fa3b unwrap: Whitespace fixes. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad e780bd7a5a unwrap: refactor tests. 
Update imports to skimage
Use simple test functions, do not wrap in a class
Whitespace fixes
 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 05419e49c4 Make unwrap visible in the exposure package. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 0df05f6048 unwrap: Use new imports in python module. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 011ea024c9 unwrap: Add setup script to build extensions. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 3bd60446a2 unwrap: Rename cython files to skimage conventions. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 4c84106b26 unwrap: Remove executable bit. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 4aa1bfb0ba unwrap: Delete old setup script. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad 5692989a11 unwrap: Move files to skimage directory tree. 2013-11-22 10:42:28 +01:00
Jostein Bø Fløystad eff276c99b Bug: Fix label sequence in regionprops. 
Closes gh-806.
 2013-10-29 11:58:59 +01:00
Jostein Bø Fløystad 8796262b0b doc: Allow specifying python binary. 2013-07-15 14:01:10 +02:00
Jostein Bø Fløystad 7e9ae43ae9 docs: Makefile respects variables from environment. 2013-07-15 13:57:35 +02:00
Jostein Bø Fløystad d5b72f91ab iradon: Do not suppress 0 frequency for filter=None. 2013-07-14 17:40:17 +02:00
Jostein Bø Fløystad 4549204507 iradon: Clean up filter code. 2013-07-14 17:39:48 +02:00
Jostein Bø Fløystad 60444ee4d3 Radon transform: PEP8 fixes. 2013-07-13 20:32:15 +02:00
Jostein Bø Fløystad 462173a53a Radon transform: Include boundary in reconstruction circle. 
A test criterion needed to be relaxed slightly to have tests still
passing. This is ok, as the reconstruction circle is now larger, meaning
larger errors should be expected. Moreover, the test in question uses
random data, and changing the seed causes greater changes in accuracy
than the amount the test criterion was relaxed by.
 2013-07-13 20:32:15 +02:00
Jostein Bø Fløystad 288ee69483 radon: Correct docstring of order_angles_golden_ratio. 2013-07-13 20:32:15 +02:00
Jostein Bø Fløystad 41c6f6d740 radon: Reduce duplication; simplifications. 2013-07-13 20:32:13 +02:00
Jostein Bø Fløystad 47b6d0c5a6 Radon transform: Document rotation axis location. 2013-07-13 20:31:28 +02:00
Jostein Bø Fløystad 2bfaafd9e2 Radon transform: Redefine projection center for sinograms. 
This definition is chosen because it is simple to express in the
documentation. No changes in accuracy are to be expected, but comparing
sinograms and reconstructions before and after this commit will give
different results in the cases where ``circle=False`` for ``radon`` or
``iradon``.
 2013-07-13 19:31:43 +02:00
Jostein Bø Fløystad 09cfe0b929 examples: Avoid python3-specific syntax. 
from __future__ import ... is ineffective when the example script is
exec-ed by sphinx, resulting in a SyntaxError when running under
python2.

Fixes gh-649.
 2013-07-12 12:52:26 +02:00
Jostein Bø Fløystad 4d307f5315 iradon_sart: Fix docstring typo. 2013-07-09 11:44:28 +02:00
Jostein Bø Fløystad 1cc42bd943 iradon_sart: Reformat references. 2013-07-09 11:44:03 +02:00
Jostein Bø Fløystad 18a06a0add iradon_sart: Format docs correctly. 2013-07-08 14:50:06 +02:00
Jostein Bø Fløystad bea50aa608 iradon: use util.pad for sinogram padding. 2013-07-06 20:55:54 +02:00
Jostein Bø Fløystad b3746b9090 iradon: Cleanup by locating related code in one place. 2013-07-06 20:55:54 +02:00
Jostein Bø Fløystad 643a1bc1f5 iradon: Add test for cubic interpolation. 2013-07-06 20:55:53 +02:00
Jostein Bø Fløystad b90ba783ef iradon: Only allow interpolation methods working well. 
Of the interpolation methods provided by scipy.interpolate.interp1d,
only cubic has been found to work well with the tests in skimage (other
methods are either identical to linear or nearest, or they produce bad
reconstructions).
 2013-07-06 20:55:53 +02:00
Jostein Bø Fløystad 2be327815e radon: Use numpy.interp/scipy.interpolate. 
Scipy supports all interpolation kinds (nearest, linear) we need, while
numpy supports only linear interpolation. The numpy interpolation is
substantially faster, so this is used even though it complicates the
code slightly.
 2013-07-06 20:55:53 +02:00
Jostein Bø Fløystad 5955e4e612 iradon: Reduce code duplication. 2013-07-06 20:55:53 +02:00
Jostein Bø Fløystad ac460a9777 iradon: Use util.pad for array padding. 
This depends on util.pad accepting 0s in pad_width, which has a proposed
solution in gh-634.
 2013-07-06 20:55:53 +02:00
Jostein Bø Fløystad 237fb989b0 radon: Use util.pad for array padding. 2013-07-06 20:55:53 +02:00
Jostein Bø Fløystad 794a4d7dae arraypad: allow padding with zero entries (i.e. no padding). 2013-07-05 14:29:09 +02:00
Jostein Bø Fløystad 553767122b Add SART to contributors. 2013-07-05 13:36:55 +02:00
Jostein Bø Fløystad 3cdfeccc7a iradon_sart: flip signs to reflect changes to radon. 
The changes to radon were introduced in gh-596.
 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad af47941435 iradon_sart: fix comment spelling. 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad f2790d658c iradon_sart: redefine projection center. 
This reflects the bugfixes related to issue gh-592 implemented in
gh-596.
 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad 06857d3b92 Radon tests: Check the correct error metric. 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad e2a0f7fff8 Radon example: Declare UTF-8 encoding. 
This is needed for non-ASCII characters in the references to papers
cited in the text.
 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad 789c19923d Radon example: print RMS errors of the reconstructions. 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad 1d611878a6 Radon example: Style fixes. 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad e5dfcb0ab4 Improve the text in and add references to the Radon example. 
Based on comments from Emmanuelle.
 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad 9e11e453b6 radon example: Display plots when run from command line. 
Call to matplotlib's show() was missing.
 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad a4870242b6 iradon_sart: Test clip functionality and add a test for it. 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad a5df8d4630 Rewrite Radon example; include SART. 
The old example had some flaws. The new example corrects these, expands
on the topic and adds content relating to the newly implemented SART
algorithm.
 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad dde4288865 test_radon_transform: Style fixes. 2013-07-05 13:14:39 +02:00
Jostein Bø Fløystad 266b202226 iradon_sart: Style fixes. 2013-07-05 13:14:38 +02:00
Jostein Bø Fløystad 116e1dd571 iradon_sart: Also test accuracy with a missing wedge. 2013-07-05 13:14:38 +02:00